Starting phenix.real_space_refine on Wed Feb 4 02:08:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kug_62578/02_2026/9kug_62578.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kug_62578/02_2026/9kug_62578.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kug_62578/02_2026/9kug_62578.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kug_62578/02_2026/9kug_62578.map" model { file = "/net/cci-nas-00/data/ceres_data/9kug_62578/02_2026/9kug_62578.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kug_62578/02_2026/9kug_62578.cif" } resolution = 3.07 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= -0.000 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 5281 2.51 5 N 1423 2.21 5 O 1496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8247 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2192 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 13, 'TRANS': 270} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 45 Chain: "B" Number of atoms: 1519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1519 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 37} Link IDs: {'PTRANS': 4, 'TRANS': 203} Chain breaks: 2 Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 10, 'ASN:plan1': 2, 'HIS:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 76 Chain: "C" Number of atoms: 2416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2416 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 236 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLU:plan': 6, 'GLN:plan1': 7, 'ARG:plan': 6, 'ASP:plan': 10, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 124 Chain: "G" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 376 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 22 Chain: "H" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1657 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1, 'GLU:plan': 7, 'ASP:plan': 3, 'PHE:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 72 Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 70 Classifications: {'peptide': 8} Link IDs: {'NMTRANS': 1, 'PTRANS': 1, 'TRANS': 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MLE:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 17 Classifications: {'peptide': 2} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 1} Time building chain proxies: 1.79, per 1000 atoms: 0.22 Number of scatterers: 8247 At special positions: 0 Unit cell: (90.705, 128.196, 134.243, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 47 16.00 O 1496 8.00 N 1423 7.00 C 5281 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 301.0 milliseconds 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DAL D 9 " Number of C-beta restraints generated: 2102 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 15 sheets defined 35.9% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 36 through 53 removed outlier: 4.088A pdb=" N LEU A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 65 removed outlier: 3.705A pdb=" N PHE A 64 " --> pdb=" O TRP A 60 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU A 65 " --> pdb=" O VAL A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 71 No H-bonds generated for 'chain 'A' and resid 69 through 71' Processing helix chain 'A' and resid 72 through 89 Processing helix chain 'A' and resid 91 through 98 removed outlier: 3.625A pdb=" N GLN A 98 " --> pdb=" O THR A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 140 Proline residue: A 113 - end of helix removed outlier: 3.833A pdb=" N ASN A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N MET A 120 " --> pdb=" O ILE A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 147 Processing helix chain 'A' and resid 149 through 169 removed outlier: 3.879A pdb=" N ALA A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 232 removed outlier: 3.805A pdb=" N ILE A 204 " --> pdb=" O ARG A 200 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N TRP A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) Proline residue: A 214 - end of helix removed outlier: 4.342A pdb=" N ARG A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 266 removed outlier: 4.156A pdb=" N LYS A 242 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Proline residue: A 257 - end of helix Processing helix chain 'A' and resid 274 through 304 removed outlier: 4.092A pdb=" N LEU A 278 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N SER A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LEU A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ASN A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N CYS A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N CYS A 294 " --> pdb=" O TYR A 290 " (cutoff:3.500A) Proline residue: A 297 - end of helix removed outlier: 4.177A pdb=" N TYR A 300 " --> pdb=" O ASN A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 315 removed outlier: 3.996A pdb=" N ARG A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS A 313 " --> pdb=" O GLY A 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 31 removed outlier: 4.011A pdb=" N ALA B 12 " --> pdb=" O GLU B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 54 Processing helix chain 'B' and resid 208 through 212 Processing helix chain 'B' and resid 213 through 217 removed outlier: 3.520A pdb=" N GLU B 217 " --> pdb=" O HIS B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 256 Processing helix chain 'B' and resid 271 through 282 Processing helix chain 'B' and resid 283 through 287 removed outlier: 3.853A pdb=" N ILE B 286 " --> pdb=" O PRO B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 310 Processing helix chain 'B' and resid 330 through 352 removed outlier: 3.514A pdb=" N GLY B 352 " --> pdb=" O LEU B 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 24 Processing helix chain 'C' and resid 29 through 35 removed outlier: 3.668A pdb=" N ILE C 33 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 23 Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.630A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.737A pdb=" N SER H 31 " --> pdb=" O ALA H 28 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 175 through 179 removed outlier: 3.744A pdb=" N VAL A 176 " --> pdb=" O GLY A 189 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG A 178 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU A 187 " --> pdb=" O ARG A 178 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 186 through 191 removed outlier: 3.677A pdb=" N PHE B 190 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA B 221 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ILE B 222 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE B 265 " --> pdb=" O TYR B 320 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 225 through 227 Processing sheet with id=AA4, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.685A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.976A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP C 82 " --> pdb=" O LEU C 70 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE C 81 " --> pdb=" O HIS C 91 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.931A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG C 137 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.655A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.877A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.602A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG C 251 " --> pdb=" O THR C 243 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 273 through 278 removed outlier: 4.077A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN C 295 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.592A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER H 7 " --> pdb=" O SER H 21 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AB4, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.641A pdb=" N SER H 99 " --> pdb=" O GLY H 33 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 140 through 141 removed outlier: 3.767A pdb=" N ALA H 211 " --> pdb=" O SER H 208 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 146 through 148 removed outlier: 3.735A pdb=" N GLU H 246 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY H 225 " --> pdb=" O LEU H 245 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE H 189 " --> pdb=" O TRP H 176 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) 383 hydrogen bonds defined for protein. 1083 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: 0.92 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2659 1.34 - 1.46: 1746 1.46 - 1.58: 3960 1.58 - 1.70: 0 1.70 - 1.81: 61 Bond restraints: 8426 Sorted by residual: bond pdb=" CA MLE D 8 " pdb=" C MLE D 8 " ideal model delta sigma weight residual 1.525 1.568 -0.043 2.10e-02 2.27e+03 4.14e+00 bond pdb=" C MLE D 8 " pdb=" O MLE D 8 " ideal model delta sigma weight residual 1.231 1.262 -0.031 2.00e-02 2.50e+03 2.39e+00 bond pdb=" CA ASN A 296 " pdb=" C ASN A 296 " ideal model delta sigma weight residual 1.524 1.538 -0.015 1.26e-02 6.30e+03 1.34e+00 bond pdb=" N PRO H 236 " pdb=" CA PRO H 236 " ideal model delta sigma weight residual 1.469 1.483 -0.014 1.28e-02 6.10e+03 1.17e+00 bond pdb=" C LEU A 117 " pdb=" O LEU A 117 " ideal model delta sigma weight residual 1.236 1.246 -0.010 1.29e-02 6.01e+03 5.82e-01 ... (remaining 8421 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 11346 1.69 - 3.38: 117 3.38 - 5.07: 19 5.07 - 6.76: 5 6.76 - 8.46: 3 Bond angle restraints: 11490 Sorted by residual: angle pdb=" N ASN A 296 " pdb=" CA ASN A 296 " pdb=" C ASN A 296 " ideal model delta sigma weight residual 109.81 118.27 -8.46 2.21e+00 2.05e-01 1.46e+01 angle pdb=" C SER A 237 " pdb=" N THR A 238 " pdb=" CA THR A 238 " ideal model delta sigma weight residual 121.54 127.15 -5.61 1.91e+00 2.74e-01 8.63e+00 angle pdb=" CA ASN A 296 " pdb=" C ASN A 296 " pdb=" N PRO A 297 " ideal model delta sigma weight residual 118.44 122.67 -4.23 1.59e+00 3.96e-01 7.08e+00 angle pdb=" N ILE A 169 " pdb=" CA ILE A 169 " pdb=" C ILE A 169 " ideal model delta sigma weight residual 108.88 114.36 -5.48 2.16e+00 2.14e-01 6.44e+00 angle pdb=" C TYR H 235 " pdb=" N PRO H 236 " pdb=" CA PRO H 236 " ideal model delta sigma weight residual 119.84 116.76 3.08 1.25e+00 6.40e-01 6.08e+00 ... (remaining 11485 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 4445 17.20 - 34.40: 385 34.40 - 51.60: 77 51.60 - 68.80: 3 68.80 - 86.00: 4 Dihedral angle restraints: 4914 sinusoidal: 1657 harmonic: 3257 Sorted by residual: dihedral pdb=" CB CYS A 109 " pdb=" SG CYS A 109 " pdb=" SG CYS A 188 " pdb=" CB CYS A 188 " ideal model delta sinusoidal sigma weight residual -86.00 -160.23 74.23 1 1.00e+01 1.00e-02 6.99e+01 dihedral pdb=" CA PRO A 183 " pdb=" C PRO A 183 " pdb=" N PRO A 184 " pdb=" CA PRO A 184 " ideal model delta harmonic sigma weight residual -180.00 -157.96 -22.04 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA ALA C 56 " pdb=" C ALA C 56 " pdb=" N LYS C 57 " pdb=" CA LYS C 57 " ideal model delta harmonic sigma weight residual 180.00 158.24 21.76 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 4911 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1094 0.050 - 0.099: 208 0.099 - 0.149: 47 0.149 - 0.199: 0 0.199 - 0.248: 1 Chirality restraints: 1350 Sorted by residual: chirality pdb=" CA ASN A 296 " pdb=" N ASN A 296 " pdb=" C ASN A 296 " pdb=" CB ASN A 296 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA ILE C 93 " pdb=" N ILE C 93 " pdb=" C ILE C 93 " pdb=" CB ILE C 93 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CA VAL A 35 " pdb=" N VAL A 35 " pdb=" C VAL A 35 " pdb=" CB VAL A 35 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.73e-01 ... (remaining 1347 not shown) Planarity restraints: 1457 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 35 " 0.041 5.00e-02 4.00e+02 6.19e-02 6.13e+00 pdb=" N PRO A 36 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 36 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 36 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 269 " 0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO A 270 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 270 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 270 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR H 235 " -0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO H 236 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO H 236 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO H 236 " -0.023 5.00e-02 4.00e+02 ... (remaining 1454 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1873 2.79 - 3.32: 7141 3.32 - 3.84: 12218 3.84 - 4.37: 13252 4.37 - 4.90: 25083 Nonbonded interactions: 59567 Sorted by model distance: nonbonded pdb=" O GLN C 75 " pdb=" OG SER C 98 " model vdw 2.259 3.040 nonbonded pdb=" NH1 ARG B 15 " pdb=" O VAL C 90 " model vdw 2.278 3.120 nonbonded pdb=" NE2 GLN A 98 " pdb=" O HIS A 101 " model vdw 2.338 3.120 nonbonded pdb=" NH2 ARG H 202 " pdb=" OE2 GLU H 220 " model vdw 2.402 3.120 nonbonded pdb=" NH2 ARG C 256 " pdb=" OD2 ASP G 36 " model vdw 2.420 3.120 ... (remaining 59562 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.680 Find NCS groups from input model: 0.020 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 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 0.100 8430 Z= 0.148 Angle : 0.488 8.455 11496 Z= 0.255 Chirality : 0.040 0.248 1350 Planarity : 0.004 0.062 1457 Dihedral : 12.969 86.000 2803 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.26), residues: 1107 helix: 2.28 (0.28), residues: 363 sheet: -0.06 (0.31), residues: 285 loop : -1.60 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 178 TYR 0.008 0.001 TYR H 190 PHE 0.010 0.001 PHE A 48 TRP 0.009 0.001 TRP A 74 HIS 0.002 0.000 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00187 ( 8426) covalent geometry : angle 0.48750 (11490) SS BOND : bond 0.00356 ( 3) SS BOND : angle 0.65734 ( 6) hydrogen bonds : bond 0.19460 ( 383) hydrogen bonds : angle 5.96885 ( 1083) Misc. bond : bond 0.09995 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 145 GLN cc_start: 0.8214 (tt0) cc_final: 0.7958 (tt0) REVERT: A 159 VAL cc_start: 0.7654 (t) cc_final: 0.7428 (t) REVERT: A 197 ARG cc_start: 0.7576 (ttt180) cc_final: 0.7360 (ttm-80) REVERT: B 24 LYS cc_start: 0.8268 (ttpt) cc_final: 0.7977 (ttpt) REVERT: B 35 LYS cc_start: 0.8495 (mtmm) cc_final: 0.8203 (mtmm) REVERT: B 185 ILE cc_start: 0.7451 (mm) cc_final: 0.7200 (tt) REVERT: B 211 LYS cc_start: 0.8167 (mmpt) cc_final: 0.7905 (mmmt) REVERT: B 279 ILE cc_start: 0.8307 (tt) cc_final: 0.8088 (tt) REVERT: B 290 GLU cc_start: 0.7824 (mp0) cc_final: 0.7580 (mp0) REVERT: C 219 ARG cc_start: 0.6960 (mmt90) cc_final: 0.6754 (mtp85) REVERT: C 247 ASP cc_start: 0.6120 (t0) cc_final: 0.5733 (t0) REVERT: C 254 ASP cc_start: 0.7008 (t70) cc_final: 0.6766 (t0) REVERT: C 291 ASP cc_start: 0.6549 (t0) cc_final: 0.6165 (t0) REVERT: C 298 ASP cc_start: 0.7306 (t0) cc_final: 0.6826 (t0) REVERT: C 322 ASP cc_start: 0.8135 (m-30) cc_final: 0.7921 (m-30) REVERT: H 60 TYR cc_start: 0.8740 (m-80) cc_final: 0.8317 (m-80) REVERT: H 202 ARG cc_start: 0.8215 (mtm110) cc_final: 0.7642 (mtp180) REVERT: D 5 ASP cc_start: 0.8162 (t0) cc_final: 0.7805 (t0) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.1174 time to fit residues: 28.8996 Evaluate side-chains 157 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS B 347 ASN C 16 ASN C 35 ASN H 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.113663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.098963 restraints weight = 12952.971| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.05 r_work: 0.3154 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8430 Z= 0.175 Angle : 0.598 8.367 11496 Z= 0.318 Chirality : 0.043 0.142 1350 Planarity : 0.005 0.061 1457 Dihedral : 4.286 21.959 1205 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.63 % Allowed : 9.27 % Favored : 89.10 % 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: 0.13 (0.26), residues: 1107 helix: 2.19 (0.28), residues: 367 sheet: 0.05 (0.31), residues: 286 loop : -1.72 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 68 TYR 0.016 0.002 TYR H 235 PHE 0.020 0.002 PHE A 135 TRP 0.015 0.001 TRP C 211 HIS 0.006 0.001 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 8426) covalent geometry : angle 0.59690 (11490) SS BOND : bond 0.01059 ( 3) SS BOND : angle 1.83831 ( 6) hydrogen bonds : bond 0.06526 ( 383) hydrogen bonds : angle 4.44664 ( 1083) Misc. bond : bond 0.00135 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 167 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: A 91 ILE cc_start: 0.8260 (mm) cc_final: 0.8042 (mt) REVERT: A 125 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7071 (mt) REVERT: A 159 VAL cc_start: 0.7897 (t) cc_final: 0.7650 (t) REVERT: A 185 LYS cc_start: 0.7597 (mmmm) cc_final: 0.7392 (tptm) REVERT: A 197 ARG cc_start: 0.8402 (ttt180) cc_final: 0.8180 (ttm-80) REVERT: B 24 LYS cc_start: 0.8394 (ttpt) cc_final: 0.8101 (ttpt) REVERT: B 35 LYS cc_start: 0.8720 (mtmm) cc_final: 0.8472 (mtmm) REVERT: B 185 ILE cc_start: 0.7855 (mm) cc_final: 0.7613 (tt) REVERT: B 211 LYS cc_start: 0.8534 (mmpt) cc_final: 0.8235 (mmmt) REVERT: B 217 GLU cc_start: 0.7885 (tt0) cc_final: 0.7576 (mt-10) REVERT: B 296 THR cc_start: 0.8353 (t) cc_final: 0.8122 (p) REVERT: C 59 TYR cc_start: 0.8735 (m-80) cc_final: 0.8437 (m-80) REVERT: C 219 ARG cc_start: 0.7800 (mmt90) cc_final: 0.7520 (mtp85) REVERT: C 247 ASP cc_start: 0.6976 (t0) cc_final: 0.6492 (t0) REVERT: C 304 ARG cc_start: 0.8422 (ttp-170) cc_final: 0.6832 (mmt-90) REVERT: G 41 CYS cc_start: 0.8056 (m) cc_final: 0.7768 (m) REVERT: H 60 TYR cc_start: 0.8912 (m-80) cc_final: 0.8480 (m-80) REVERT: H 202 ARG cc_start: 0.8397 (mtm110) cc_final: 0.7859 (mtp180) REVERT: H 219 LEU cc_start: 0.8060 (tp) cc_final: 0.7833 (tt) REVERT: D 5 ASP cc_start: 0.8331 (t0) cc_final: 0.7909 (t0) outliers start: 13 outliers final: 10 residues processed: 171 average time/residue: 0.1211 time to fit residues: 26.0711 Evaluate side-chains 170 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 159 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain H residue 226 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 347 ASN C 16 ASN C 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.112947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.098448 restraints weight = 12888.674| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.02 r_work: 0.3146 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8430 Z= 0.171 Angle : 0.587 10.305 11496 Z= 0.313 Chirality : 0.043 0.138 1350 Planarity : 0.005 0.060 1457 Dihedral : 4.359 22.753 1205 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.26 % Allowed : 12.66 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.26), residues: 1107 helix: 2.20 (0.28), residues: 367 sheet: 0.06 (0.30), residues: 292 loop : -1.79 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 42 TYR 0.019 0.002 TYR H 235 PHE 0.018 0.002 PHE A 135 TRP 0.015 0.002 TRP C 211 HIS 0.004 0.001 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 8426) covalent geometry : angle 0.58510 (11490) SS BOND : bond 0.01051 ( 3) SS BOND : angle 1.88610 ( 6) hydrogen bonds : bond 0.06307 ( 383) hydrogen bonds : angle 4.33759 ( 1083) Misc. bond : bond 0.00131 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: A 91 ILE cc_start: 0.8247 (mm) cc_final: 0.8014 (mt) REVERT: A 125 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.7133 (mt) REVERT: A 159 VAL cc_start: 0.7894 (t) cc_final: 0.7644 (t) REVERT: A 197 ARG cc_start: 0.8393 (ttt180) cc_final: 0.8174 (ttm-80) REVERT: B 24 LYS cc_start: 0.8390 (ttpt) cc_final: 0.8127 (ttpt) REVERT: B 35 LYS cc_start: 0.8667 (mtmm) cc_final: 0.8430 (mtmm) REVERT: B 185 ILE cc_start: 0.7818 (mm) cc_final: 0.7573 (tt) REVERT: B 217 GLU cc_start: 0.7873 (tt0) cc_final: 0.7566 (mt-10) REVERT: B 296 THR cc_start: 0.8361 (t) cc_final: 0.8128 (p) REVERT: C 59 TYR cc_start: 0.8704 (m-80) cc_final: 0.8478 (m-80) REVERT: C 247 ASP cc_start: 0.7034 (t0) cc_final: 0.6573 (t0) REVERT: C 304 ARG cc_start: 0.8451 (ttp-170) cc_final: 0.6850 (mmt-90) REVERT: G 41 CYS cc_start: 0.8048 (m) cc_final: 0.7777 (m) REVERT: H 60 TYR cc_start: 0.8910 (m-80) cc_final: 0.8460 (m-80) REVERT: H 230 MET cc_start: 0.8561 (ttp) cc_final: 0.8151 (ttt) REVERT: D 5 ASP cc_start: 0.8316 (t0) cc_final: 0.7895 (t0) outliers start: 18 outliers final: 15 residues processed: 162 average time/residue: 0.1021 time to fit residues: 21.6197 Evaluate side-chains 165 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 226 VAL Chi-restraints excluded: chain H residue 245 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 20 optimal weight: 0.1980 chunk 56 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 88 optimal weight: 0.0980 chunk 95 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 347 ASN C 16 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.113929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.099251 restraints weight = 13151.622| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.06 r_work: 0.3158 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8430 Z= 0.137 Angle : 0.541 9.531 11496 Z= 0.289 Chirality : 0.042 0.137 1350 Planarity : 0.004 0.061 1457 Dihedral : 4.194 22.464 1205 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.38 % Allowed : 14.66 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.26), residues: 1107 helix: 2.33 (0.28), residues: 367 sheet: 0.15 (0.31), residues: 292 loop : -1.74 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 68 TYR 0.015 0.001 TYR H 235 PHE 0.014 0.001 PHE A 135 TRP 0.013 0.001 TRP C 211 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 8426) covalent geometry : angle 0.54013 (11490) SS BOND : bond 0.00875 ( 3) SS BOND : angle 1.61960 ( 6) hydrogen bonds : bond 0.05523 ( 383) hydrogen bonds : angle 4.16609 ( 1083) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 91 ILE cc_start: 0.8246 (mm) cc_final: 0.8006 (mt) REVERT: A 159 VAL cc_start: 0.7865 (t) cc_final: 0.7615 (t) REVERT: A 197 ARG cc_start: 0.8351 (ttt180) cc_final: 0.7932 (tpp80) REVERT: B 24 LYS cc_start: 0.8374 (ttpt) cc_final: 0.8110 (ttpt) REVERT: B 35 LYS cc_start: 0.8627 (mtmm) cc_final: 0.8379 (mtmm) REVERT: B 185 ILE cc_start: 0.7827 (mm) cc_final: 0.7550 (tt) REVERT: B 217 GLU cc_start: 0.7857 (tt0) cc_final: 0.7536 (mt-10) REVERT: B 290 GLU cc_start: 0.8154 (mp0) cc_final: 0.7820 (mp0) REVERT: B 296 THR cc_start: 0.8365 (t) cc_final: 0.8086 (p) REVERT: C 247 ASP cc_start: 0.6976 (t0) cc_final: 0.6502 (t0) REVERT: C 304 ARG cc_start: 0.8471 (ttp-170) cc_final: 0.6829 (mmt-90) REVERT: G 41 CYS cc_start: 0.8072 (m) cc_final: 0.7773 (m) REVERT: H 60 TYR cc_start: 0.8880 (m-80) cc_final: 0.8401 (m-80) REVERT: H 230 MET cc_start: 0.8561 (ttp) cc_final: 0.8143 (ttt) REVERT: D 5 ASP cc_start: 0.8286 (t0) cc_final: 0.7889 (t0) outliers start: 19 outliers final: 15 residues processed: 165 average time/residue: 0.1012 time to fit residues: 21.5750 Evaluate side-chains 172 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain H residue 197 SER Chi-restraints excluded: chain H residue 226 VAL Chi-restraints excluded: chain H residue 245 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 98 optimal weight: 0.0670 chunk 18 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 103 optimal weight: 0.3980 chunk 32 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 45 optimal weight: 0.5980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 347 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.115041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.100300 restraints weight = 13102.349| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.07 r_work: 0.3178 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8430 Z= 0.120 Angle : 0.518 9.042 11496 Z= 0.275 Chirality : 0.041 0.135 1350 Planarity : 0.004 0.063 1457 Dihedral : 4.030 22.336 1205 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.76 % Allowed : 15.79 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.26), residues: 1107 helix: 2.44 (0.28), residues: 367 sheet: 0.24 (0.31), residues: 292 loop : -1.69 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 68 TYR 0.012 0.001 TYR H 190 PHE 0.011 0.001 PHE C 253 TRP 0.012 0.001 TRP C 211 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 8426) covalent geometry : angle 0.51740 (11490) SS BOND : bond 0.00747 ( 3) SS BOND : angle 1.39185 ( 6) hydrogen bonds : bond 0.04938 ( 383) hydrogen bonds : angle 4.00349 ( 1083) Misc. bond : bond 0.00023 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: A 91 ILE cc_start: 0.8211 (mm) cc_final: 0.7968 (mt) REVERT: A 159 VAL cc_start: 0.7826 (t) cc_final: 0.7582 (t) REVERT: A 197 ARG cc_start: 0.8337 (ttt180) cc_final: 0.7909 (tpp80) REVERT: B 24 LYS cc_start: 0.8413 (ttpt) cc_final: 0.8145 (ttpt) REVERT: B 35 LYS cc_start: 0.8657 (mtmm) cc_final: 0.8419 (mtmm) REVERT: B 185 ILE cc_start: 0.7834 (mm) cc_final: 0.7573 (tt) REVERT: B 217 GLU cc_start: 0.7812 (tt0) cc_final: 0.7510 (mt-10) REVERT: B 290 GLU cc_start: 0.8159 (mp0) cc_final: 0.7870 (mp0) REVERT: B 307 GLN cc_start: 0.8285 (mm-40) cc_final: 0.8050 (mm-40) REVERT: C 234 PHE cc_start: 0.8772 (OUTLIER) cc_final: 0.8140 (m-80) REVERT: C 247 ASP cc_start: 0.6906 (t0) cc_final: 0.6424 (t0) REVERT: C 304 ARG cc_start: 0.8456 (ttp-170) cc_final: 0.6821 (mmt-90) REVERT: G 41 CYS cc_start: 0.8041 (m) cc_final: 0.7727 (m) REVERT: H 60 TYR cc_start: 0.8850 (m-80) cc_final: 0.8397 (m-80) REVERT: H 230 MET cc_start: 0.8581 (ttp) cc_final: 0.8144 (ttt) REVERT: D 5 ASP cc_start: 0.8298 (t0) cc_final: 0.7909 (t0) outliers start: 22 outliers final: 17 residues processed: 166 average time/residue: 0.1044 time to fit residues: 22.5789 Evaluate side-chains 170 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain H residue 197 SER Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 226 VAL Chi-restraints excluded: chain H residue 245 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 3 optimal weight: 3.9990 chunk 38 optimal weight: 0.2980 chunk 47 optimal weight: 0.8980 chunk 43 optimal weight: 0.4980 chunk 86 optimal weight: 0.9980 chunk 20 optimal weight: 0.1980 chunk 56 optimal weight: 0.0170 chunk 102 optimal weight: 0.6980 chunk 88 optimal weight: 0.2980 chunk 50 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.2618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 347 ASN C 16 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.117031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.102215 restraints weight = 13033.436| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.07 r_work: 0.3209 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8430 Z= 0.099 Angle : 0.492 9.368 11496 Z= 0.257 Chirality : 0.040 0.132 1350 Planarity : 0.004 0.061 1457 Dihedral : 3.800 21.425 1205 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.88 % Allowed : 15.91 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.26), residues: 1107 helix: 2.54 (0.28), residues: 367 sheet: 0.39 (0.31), residues: 292 loop : -1.60 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 219 TYR 0.011 0.001 TYR H 190 PHE 0.009 0.001 PHE A 48 TRP 0.012 0.001 TRP C 211 HIS 0.001 0.000 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 8426) covalent geometry : angle 0.49119 (11490) SS BOND : bond 0.00636 ( 3) SS BOND : angle 1.14960 ( 6) hydrogen bonds : bond 0.04108 ( 383) hydrogen bonds : angle 3.82079 ( 1083) Misc. bond : bond 0.00018 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 125 LEU cc_start: 0.6980 (OUTLIER) cc_final: 0.6551 (mt) REVERT: A 159 VAL cc_start: 0.7818 (t) cc_final: 0.7577 (t) REVERT: A 197 ARG cc_start: 0.8265 (ttt180) cc_final: 0.7821 (tpp80) REVERT: B 24 LYS cc_start: 0.8448 (ttpt) cc_final: 0.8142 (ttpt) REVERT: B 35 LYS cc_start: 0.8624 (mtmm) cc_final: 0.8378 (mtmm) REVERT: B 185 ILE cc_start: 0.7808 (mm) cc_final: 0.7595 (tt) REVERT: B 217 GLU cc_start: 0.7787 (tt0) cc_final: 0.7498 (mt-10) REVERT: B 290 GLU cc_start: 0.8148 (mp0) cc_final: 0.7861 (mp0) REVERT: C 234 PHE cc_start: 0.8758 (OUTLIER) cc_final: 0.8181 (m-80) REVERT: C 247 ASP cc_start: 0.6690 (t0) cc_final: 0.6193 (t0) REVERT: C 304 ARG cc_start: 0.8447 (ttp-170) cc_final: 0.6816 (mmt-90) REVERT: H 60 TYR cc_start: 0.8807 (m-80) cc_final: 0.8364 (m-80) REVERT: H 67 ARG cc_start: 0.8401 (ttp-170) cc_final: 0.8154 (ttp-170) REVERT: H 91 THR cc_start: 0.8641 (OUTLIER) cc_final: 0.8322 (t) REVERT: D 5 ASP cc_start: 0.8269 (t0) cc_final: 0.7890 (t0) outliers start: 23 outliers final: 17 residues processed: 161 average time/residue: 0.1141 time to fit residues: 23.5834 Evaluate side-chains 166 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain H residue 197 SER Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 226 VAL Chi-restraints excluded: chain H residue 245 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 88 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 347 ASN C 16 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.112856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.098312 restraints weight = 13011.055| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.03 r_work: 0.3143 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8430 Z= 0.170 Angle : 0.581 9.431 11496 Z= 0.306 Chirality : 0.043 0.153 1350 Planarity : 0.005 0.063 1457 Dihedral : 4.261 23.390 1205 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.51 % Allowed : 15.79 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.26), residues: 1107 helix: 2.44 (0.28), residues: 367 sheet: 0.28 (0.31), residues: 295 loop : -1.71 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 219 TYR 0.013 0.002 TYR H 235 PHE 0.021 0.002 PHE A 135 TRP 0.013 0.001 TRP C 211 HIS 0.004 0.001 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 8426) covalent geometry : angle 0.58000 (11490) SS BOND : bond 0.01113 ( 3) SS BOND : angle 1.73180 ( 6) hydrogen bonds : bond 0.06129 ( 383) hydrogen bonds : angle 4.13590 ( 1083) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: A 91 ILE cc_start: 0.8203 (mm) cc_final: 0.7983 (mt) REVERT: A 125 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.7066 (mt) REVERT: A 197 ARG cc_start: 0.8394 (ttt180) cc_final: 0.7957 (tpp80) REVERT: B 24 LYS cc_start: 0.8374 (ttpt) cc_final: 0.8112 (ttpt) REVERT: B 35 LYS cc_start: 0.8683 (mtmm) cc_final: 0.8447 (mtmm) REVERT: B 185 ILE cc_start: 0.7854 (mm) cc_final: 0.7603 (tt) REVERT: B 217 GLU cc_start: 0.7850 (tt0) cc_final: 0.7545 (mt-10) REVERT: B 290 GLU cc_start: 0.8153 (mp0) cc_final: 0.7898 (mp0) REVERT: B 296 THR cc_start: 0.8371 (t) cc_final: 0.8090 (p) REVERT: C 59 TYR cc_start: 0.8673 (m-80) cc_final: 0.8408 (m-80) REVERT: C 234 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.8131 (m-80) REVERT: C 247 ASP cc_start: 0.6970 (t0) cc_final: 0.6515 (t0) REVERT: C 304 ARG cc_start: 0.8535 (ttp-170) cc_final: 0.6837 (mmt-90) REVERT: H 60 TYR cc_start: 0.8880 (m-80) cc_final: 0.8417 (m-80) REVERT: H 230 MET cc_start: 0.8553 (ttp) cc_final: 0.8176 (ttt) REVERT: D 5 ASP cc_start: 0.8279 (t0) cc_final: 0.7873 (t0) outliers start: 28 outliers final: 20 residues processed: 170 average time/residue: 0.1143 time to fit residues: 25.0819 Evaluate side-chains 173 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 197 SER Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 226 VAL Chi-restraints excluded: chain H residue 245 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 81 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 chunk 43 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 347 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.113680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.099091 restraints weight = 12970.100| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.04 r_work: 0.3156 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8430 Z= 0.143 Angle : 0.554 9.485 11496 Z= 0.292 Chirality : 0.042 0.146 1350 Planarity : 0.004 0.062 1457 Dihedral : 4.184 23.350 1205 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.01 % Allowed : 16.42 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.26), residues: 1107 helix: 2.44 (0.28), residues: 366 sheet: 0.24 (0.31), residues: 296 loop : -1.75 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 22 TYR 0.013 0.001 TYR H 235 PHE 0.015 0.002 PHE A 135 TRP 0.013 0.001 TRP C 211 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 8426) covalent geometry : angle 0.55272 (11490) SS BOND : bond 0.00938 ( 3) SS BOND : angle 1.52238 ( 6) hydrogen bonds : bond 0.05537 ( 383) hydrogen bonds : angle 4.07614 ( 1083) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: A 91 ILE cc_start: 0.8202 (mm) cc_final: 0.7972 (mt) REVERT: A 125 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6835 (mt) REVERT: A 159 VAL cc_start: 0.7877 (t) cc_final: 0.7614 (t) REVERT: A 197 ARG cc_start: 0.8387 (ttt180) cc_final: 0.7943 (tpp80) REVERT: B 24 LYS cc_start: 0.8430 (ttpt) cc_final: 0.8168 (ttpt) REVERT: B 35 LYS cc_start: 0.8652 (mtmm) cc_final: 0.8451 (mtmm) REVERT: B 185 ILE cc_start: 0.7866 (mm) cc_final: 0.7618 (tt) REVERT: B 217 GLU cc_start: 0.7835 (tt0) cc_final: 0.7524 (mt-10) REVERT: B 290 GLU cc_start: 0.8156 (mp0) cc_final: 0.7847 (mp0) REVERT: B 296 THR cc_start: 0.8356 (t) cc_final: 0.8062 (p) REVERT: C 59 TYR cc_start: 0.8653 (m-80) cc_final: 0.8437 (m-80) REVERT: C 234 PHE cc_start: 0.8735 (OUTLIER) cc_final: 0.8098 (m-80) REVERT: C 247 ASP cc_start: 0.6939 (t0) cc_final: 0.6459 (t0) REVERT: C 304 ARG cc_start: 0.8533 (ttp-170) cc_final: 0.6865 (mmt-90) REVERT: H 60 TYR cc_start: 0.8873 (m-80) cc_final: 0.8400 (m-80) REVERT: H 230 MET cc_start: 0.8535 (ttp) cc_final: 0.8160 (ttt) REVERT: D 5 ASP cc_start: 0.8274 (t0) cc_final: 0.7945 (t0) outliers start: 24 outliers final: 20 residues processed: 162 average time/residue: 0.0946 time to fit residues: 19.9731 Evaluate side-chains 170 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain H residue 197 SER Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 226 VAL Chi-restraints excluded: chain H residue 245 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 58 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 85 optimal weight: 0.0270 chunk 7 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 347 ASN C 16 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.113582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.099013 restraints weight = 12953.151| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.04 r_work: 0.3154 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8430 Z= 0.144 Angle : 0.554 9.461 11496 Z= 0.292 Chirality : 0.042 0.147 1350 Planarity : 0.004 0.063 1457 Dihedral : 4.197 23.191 1205 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.26 % Allowed : 16.29 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.26), residues: 1107 helix: 2.47 (0.28), residues: 366 sheet: 0.29 (0.31), residues: 294 loop : -1.73 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 22 TYR 0.014 0.001 TYR H 235 PHE 0.016 0.002 PHE A 135 TRP 0.013 0.001 TRP C 211 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 8426) covalent geometry : angle 0.55338 (11490) SS BOND : bond 0.00972 ( 3) SS BOND : angle 1.52314 ( 6) hydrogen bonds : bond 0.05597 ( 383) hydrogen bonds : angle 4.08823 ( 1083) Misc. bond : bond 0.00012 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: A 91 ILE cc_start: 0.8196 (mm) cc_final: 0.7967 (mt) REVERT: A 125 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6839 (mt) REVERT: A 159 VAL cc_start: 0.7877 (t) cc_final: 0.7623 (t) REVERT: A 197 ARG cc_start: 0.8397 (ttt180) cc_final: 0.7950 (tpp80) REVERT: B 35 LYS cc_start: 0.8648 (mtmm) cc_final: 0.8445 (mtmm) REVERT: B 185 ILE cc_start: 0.7870 (mm) cc_final: 0.7617 (tt) REVERT: B 217 GLU cc_start: 0.7842 (tt0) cc_final: 0.7530 (mt-10) REVERT: B 290 GLU cc_start: 0.8154 (mp0) cc_final: 0.7854 (mp0) REVERT: B 296 THR cc_start: 0.8351 (t) cc_final: 0.8056 (p) REVERT: C 59 TYR cc_start: 0.8665 (m-80) cc_final: 0.8409 (m-80) REVERT: C 234 PHE cc_start: 0.8728 (OUTLIER) cc_final: 0.8089 (m-80) REVERT: C 247 ASP cc_start: 0.6941 (t0) cc_final: 0.6463 (t0) REVERT: C 304 ARG cc_start: 0.8532 (ttp-170) cc_final: 0.6861 (mmt-90) REVERT: H 60 TYR cc_start: 0.8875 (m-80) cc_final: 0.8394 (m-80) REVERT: H 230 MET cc_start: 0.8542 (ttp) cc_final: 0.8157 (ttt) REVERT: D 5 ASP cc_start: 0.8287 (t0) cc_final: 0.7845 (t0) outliers start: 26 outliers final: 21 residues processed: 167 average time/residue: 0.1135 time to fit residues: 24.2589 Evaluate side-chains 173 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain H residue 197 SER Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 226 VAL Chi-restraints excluded: chain H residue 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 34 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 37 optimal weight: 0.0040 chunk 73 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 5 optimal weight: 0.2980 chunk 59 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 347 ASN C 16 ASN C 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.114053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.099488 restraints weight = 12897.941| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.03 r_work: 0.3163 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8430 Z= 0.136 Angle : 0.548 9.213 11496 Z= 0.288 Chirality : 0.042 0.145 1350 Planarity : 0.004 0.062 1457 Dihedral : 4.152 23.189 1205 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.13 % Allowed : 15.91 % Favored : 80.95 % 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: 0.42 (0.26), residues: 1107 helix: 2.48 (0.28), residues: 366 sheet: 0.31 (0.31), residues: 295 loop : -1.72 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 219 TYR 0.014 0.001 TYR H 235 PHE 0.014 0.001 PHE A 135 TRP 0.013 0.001 TRP C 211 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 8426) covalent geometry : angle 0.54695 (11490) SS BOND : bond 0.00906 ( 3) SS BOND : angle 1.42170 ( 6) hydrogen bonds : bond 0.05379 ( 383) hydrogen bonds : angle 4.06169 ( 1083) Misc. bond : bond 0.00008 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 91 ILE cc_start: 0.8191 (mm) cc_final: 0.7961 (mt) REVERT: A 125 LEU cc_start: 0.7150 (OUTLIER) cc_final: 0.6769 (mt) REVERT: A 159 VAL cc_start: 0.7856 (t) cc_final: 0.7602 (t) REVERT: A 197 ARG cc_start: 0.8372 (ttt180) cc_final: 0.7926 (tpp80) REVERT: B 35 LYS cc_start: 0.8635 (mtmm) cc_final: 0.8432 (mtmm) REVERT: B 185 ILE cc_start: 0.7868 (mm) cc_final: 0.7626 (tt) REVERT: B 217 GLU cc_start: 0.7818 (tt0) cc_final: 0.7518 (mt-10) REVERT: B 290 GLU cc_start: 0.8152 (mp0) cc_final: 0.7858 (mp0) REVERT: B 296 THR cc_start: 0.8337 (t) cc_final: 0.8034 (p) REVERT: C 59 TYR cc_start: 0.8644 (m-80) cc_final: 0.8391 (m-80) REVERT: C 234 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.8075 (m-80) REVERT: C 247 ASP cc_start: 0.6921 (t0) cc_final: 0.6445 (t0) REVERT: C 304 ARG cc_start: 0.8527 (ttp-170) cc_final: 0.6853 (mmt-90) REVERT: H 60 TYR cc_start: 0.8873 (m-80) cc_final: 0.8388 (m-80) REVERT: H 230 MET cc_start: 0.8548 (ttp) cc_final: 0.8161 (ttt) REVERT: D 5 ASP cc_start: 0.8275 (t0) cc_final: 0.7838 (t0) outliers start: 25 outliers final: 23 residues processed: 164 average time/residue: 0.1056 time to fit residues: 22.1941 Evaluate side-chains 176 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain H residue 197 SER Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 226 VAL Chi-restraints excluded: chain H residue 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 37 optimal weight: 0.0870 chunk 46 optimal weight: 0.7980 chunk 67 optimal weight: 0.0020 chunk 61 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 66 optimal weight: 0.0370 chunk 93 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 overall best weight: 0.3244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 347 ASN C 16 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.116246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.101393 restraints weight = 13025.076| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.08 r_work: 0.3192 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 8430 Z= 0.108 Angle : 0.512 9.234 11496 Z= 0.268 Chirality : 0.040 0.138 1350 Planarity : 0.004 0.063 1457 Dihedral : 3.901 22.198 1205 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.88 % Allowed : 16.29 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.26), residues: 1107 helix: 2.54 (0.28), residues: 366 sheet: 0.38 (0.31), residues: 293 loop : -1.59 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 219 TYR 0.012 0.001 TYR H 190 PHE 0.009 0.001 PHE A 48 TRP 0.012 0.001 TRP C 211 HIS 0.002 0.000 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 8426) covalent geometry : angle 0.51143 (11490) SS BOND : bond 0.00669 ( 3) SS BOND : angle 1.08398 ( 6) hydrogen bonds : bond 0.04449 ( 383) hydrogen bonds : angle 3.90494 ( 1083) Misc. bond : bond 0.00024 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2163.69 seconds wall clock time: 37 minutes 32.05 seconds (2252.05 seconds total)